Ebusua Dwarfs handed WAFA their first defeat in Zone B on the Special Competition on Wednesday to end the first round.
The Crabs needed a 23rd minute penalty from Albert Gaisie to edge the Academy Boys at the Cape Coast Stadium.
The referee whistle after a foul inside the WAFA box.
Dwarfs made it two straight wins after beating Inter Allies 1-0 on the road on Easter Sunday.
WAFA had earned draws at Elmina Sharks and Dreams FC in their previous away matches.